Hi

I used Aegilops repeat mask genome for Tophat2 genome option, but it showed this error:

[2015-01-20 16:07:17] Checking for Bowtie
          Bowtie version:     2.1.0.0
[2015-01-20 16:07:17] Checking for Samtools
        Samtools version:     0.1.19.0
[2015-01-20 16:07:17] Checking for Bowtie index files (genome)..
[2015-01-20 16:07:17] Checking for reference FASTA file
[2015-01-20 16:07:17] Generating SAM header for AT_rm
`Traceback (most recent call last):
  File "/usr/local/bin/tophat", line 4072, in <module>
    sys.exit(main())
  File "/usr/local/bin/tophat", line 3926, in main
    params.read_params = check_reads_format(params, reads_list)
  File "/usr/local/bin/tophat", line 1829, in check_reads_format
    zf = ZReader(f_name, params)
  File "/usr/local/bin/tophat", line 1782, in __init__
    self.file=open(filename)

How can I fix this error?

Thanks a lot.